The Ghost in the Shadows
by jenlovesbones
Summary: What if the end of Aliens in a Spaceship ended a little differently? I can't believe I'm actually writing an AU ending to the most perfect episode of the series that references one of the other best episodes of the series. *facepalm*


_**A/N: Sooooo... I have this really bad habit of writing entire stories or almost complete stories and never publishing them. And tonight, browsing my files, I came across this complete story. I reread it, really liked it, and decided to post before I over-analyze. However- I should warn that if you're filled with holiday cheer at the moment, maybe save this for another day. :)**_

**Background: My favorite Bones episode ever is Aliens in a Spaceship. Just- I have no words. So, when people write tags to it, I get all "why, why, WHY?" because you can't improve on perfection, right?**

**Of course, now I'm screwing that up by publishing a post-Aliens AU. Go. Figure. :)**

* * *

His throat burned as he drained the glass of scotch. He always switched to the cheap stuff after the first couple drinks, cause there was no point in paying for the good stuff when your tongue was too numb, your senses too impaired to taste it.

He finished it off in a gulp and returned to his regular game of rimming the glass with his finger. He would tip the glass to the left, then let it drop back to its upright position.

_Tip it right. Drop._

_Repeat._

The bartender in this joint was new to him the first night he came back here nearly six months ago. And for nearly six months, the bartender knew his pattern, knew his order. And he never asked questions.

Every goddamned other person in his life asked questions, mostly questions he didn't have or want answers to. But not Sparky.

That probably wasn't his name. But, really, he was always too drunk to care.

_Tip it left. Drop._

The racking of a new set of balls behind him drew his attention away from the glass momentarily.

He watched this group chalk their cues. He heard their smack talk to one another. He thought he felt the force of the money being slammed on to the table. Bet set.

He turned away, back to focus on his glass. In his darkest days, gambling could take away the pain.

But that was before. Before, when he thought being a good soldier his biggest sin.

But at least he was good at that. At least…

_Tip it right. Drop._

What he wasn't, it turned out, was a good cop. He had failed at that. Miserably. And people died because of it. Because of him.

_Tip it left. Drop._

She died because of him.

Which is why he returned to this stool, every night. The first time he ever drank with her, he sat here on this stool and she sat next to him. And every night since he lost her, he sat in that same place and drank with her.

_Tip it right. Drop._

Is it drink for or drink with? She would tell him that it's impossible for her to drink with him. Because obviously, she's not here.

The bartender glanced at him when he laughed at that. She may not be here, but she sure as hell was in his head. He could hear her voice. Hell, sometimes he thinks he can smell her too.

And by the sixth or seventh glass of scotch every night, he swears he can start to see her. She looks at him. She smiles. She laughs. She frowns. She does that scolding professor look so very well.

_Tip it left. Drop._

He's haunted by her. She doesn't say anything when he sees her. Neither does he.

By the time he's lost count of his drinks, she's sitting next to him, looking at him. This, he can readily admit, is the only part of any day he lives for anymore. A moment, however it comes to pass, where she's by his side.

It's different tonight, though. Tonight, she looks through him, past him. Then her hand raises quickly to his cheek. It never quite touches him, but he thinks he can almost feel it. So he closes his eyes. Her hand drifts from his cheek to his shoulder.

_Tip it right. Drop._

And he opens his eyes.

She's not there anymore. But he still feels her hand on his shoulder. Or _someone's hand_, he begins to realize in his drunken state.

He searches the entire bar for any sight of her, ignoring the hand on his shoulder. His eyes move frantically for seconds, maybe minutes, before he hears his name.

"…Booth… Agent Booth, can you hear me?"

"What?" Booth finally gasps, shoving the hand from his shoulder as he jumps to his feet. Of course, now on alert but with copious amounts of alcohol flowing through his system, jumping led to falling.

"Agent Booth, are you alright?" the man said to him, standing above him, while Booth tried to focus on anything from the floor.

"Where is she? Where'd she go?" he continued to repeat. Booth widened his eyes and shook his head in an attempt to clear the fog from his mind. When he looked at the man again, he gasped. "Zack?"

"The FBI called me, Agent Booth," Zack said as he helped Booth up and onto his stool.

"I'm not Agent Booth, anymore, squint," Booth growled, facing away from Zack and toward the bar, signaling the bartender for another drink.

"I know. That's why I had to come to this establishment to locate you. They think they found where she was buried. And I'm on my way to the scene to examine the remains."

"They found her?" he asked, stopping his fresh glass of cheap scotch before it reached his lips.

"They think so."

This time, his glass just simply dropped… to the floor.

ooooooooooooooooooooooooooooooooooooooooo

Zack was stronger than he looked and Booth was drunker than he thought, so thankfully, being dragged to the car by the kid wasn't outside the realm of the squint's capabilities. He didn't remember much of the drive. He only came to anytime the car came to a stop. It was then that his stomach would roll and he'd have to fight back a new wave of nausea.

He could make out that they were headed south, out of the city, before he finally passed out in the car for good. When he came to next, he couldn't have guessed where he was.

The sun hadn't quite set yet. But he hadn't stepped out of the bar at night while the Earth was still in the light-grasping vicinity of the sun in a long time, so this was new to him. Even nearing dusk, the world felt too bright for his psyche to tolerate.

He shouldn't be here, he thought. Somewhere, there's a stool waiting for him, in a place she once was. And if he drank long enough, he'd see her again. She would be waiting for him. And some of her… this was all he had left of her. And as his stomach rolled as the car stopped, all he wanted to do was go back to that bar for her.

"Booth?" a voice said from behind him, squinting when an overhead light from the extraction team was turned on to beam over the site.

"Camille," he said, his tone devoid of emotion.

"You look like crap, Seeley," she stated bluntly.

"Really? Cause I feel like a freaking ray of sunshine," he shot back.

"I see that you're still best friends with…" she stopped and sniffed him, before making a disgusted face. "Scotch, is it? You certainly haven't seen your friend soap in a few days."

"If the way I smell is bothering you, you can go stand someplace else… anywhere but here, really."

"You know, you should probably try and talk to someone who can help you deal with this."

He said nothing.

"I'm not saying you should go back to the FBI and I'm not saying that talking to someone will help right away. I just think…" she stopped, looking at the man who was her friend, had been her lover in the past. For weeks after the kidnapping, she had tried talking to him. She'd gone to his place, she'd forced the door open. Once, she even managed to drag his drunk ass into a shower, fully clothed, praying it would snap him out of his perpetual state of numbness. They'd barely spoken in those weeks. He wouldn't look at her. He recoiled when she attempted to touch him. And one day, she just gave up. Moved on. She wasn't proud of herself, and that like of pride manifested like anger now.

But even now, she couldn't bring herself not to care. She had been his friend, and to see him like this…. "I may not have known Doctor Brennan very well, but I know she cared about you a great deal. And, you cared for her, obviously. And she would be disappointed to see how you've handled this."

"'This' Camille. When you say 'this', you mean her murder. You mean her death. I couldn't save her. She's not here to be disappointed with me or anything else, for that matter because she's dead. And that's my fault."

"Seeley…"

"Now there's nothing left of Bones but her bones…" he murmured quietly, before he began to chuckle. And that chuckle turned in to a laugh. Which turned into a rolling holler. "Nothing left of Bones but her bones!" he repeated, laughing some more, while others at the scene looked at him, taken aback by his seemingly inappropriate reaction to the situation.

Booth continued laughing, falling to the ground finally, while Cam watched him with a mixed look of pity and sadness.

When Booth noted the pity, he ceased the laughter and his face dropped all expression. "Don't you have work to do, Camille?"

She shook her head before turning and walking away from him.

Booth sighed as he looked out from his vantage point, down the sandy embankment, toward the site of the crew. A tow truck was working to drag something out of the ground. Something that looked like the back of a car's bumper.

He continued to watch it as it pulled, trying to gain all the traction available to overpower the weight of the sediment burying the vehicle.

Booth tucked his knees into his chest and rested his head on his knees. Anyone who looked at him would have seen a grown man who resembled a scared little boy. But no one got close enough to him to see the tears start to fall.

Booth closed his eyes, hoping that the earth that had swallowed her whole would take him as well.

oooooooooooooooooooooooooooooooooooo

He didn't know how much time had passed before he was jolted from dream state to consciousness. He thought a noise had woken him, but as he looked around the site, he realized that it was eerily quiet for the number of people who were present.

Beside him, Angela sat. He hadn't seen her when he arrived. And she looked almost as good as he bet he looked. He wanted to feel bad for her. He had the sudden urge to comfort her. But he was far too exhausted to do either. So he just continued to stare straight ahead.

They sat there in silence. And waited.

It may have been minutes or hours before they both heard Zack behind them.

"Angela, Agent Booth?" he said with more caution that one would expect from Zack.

"Is it them, Zack?" Angela asked hoarsely.

Both Angela and Booth turned to face Zack as he answered.

"I've examined the remains in the car…" he said, fidgeting with his hands.

"And?" Booth asked.

ooooooooooooooooooooooooooooooooooooooooooooooooo

"And I can say with a reasonable amount of certainty that the set of remains is Hodgins… Doctor Hodgins," Zack said. Angela let out a sigh that resembled a sob, succumbing to the truth she had already known, as Booth scrubbed a hand over his face.

Behind them, they could hear Cam shouting for Zack from a distance. But their attention remained focused on Zack.

"And the other… person. The other set of remains?" Booth spat morosely.

"There wasn't… there was only one set of remains."

"What?!" both Booth and Angela exclaimed simultaneously.

"What do you mean?"

"I mean, there's only one set of remains in the car and I brought Doctor Hodgins' dental x-rays and while my cursory examination is not conclusive, as I would need to return to the lab, I am confident that the remains in the car belong to Hodgins."

"What about Bones?" Booth shouted.

"Yes, his bones were in the car," Zack answered.

"No! Bones. My Bones. Where's Brennan?!" Booth shouted, every word getting louder, which made Zack flinch.

"I don't know where Doctor Brennan is…"

"Booth!" Cam had finally reached them at a full-on sprint from the excavation site.

"Booth, I think she was in the car… at least for a little while. This was left for you."

Cam handed Booth a letter… no one said anything about the shaking hand he extended to grab it. He twirled it in his fingers for a moment, staring at the print on the outside of the envelope.

"Please deliver to FBI Special Agent Seeley Booth," Angela whispered aloud.

"Booth, open it," Cam insisted.

oooooooooooooooooooooooooooooooo

The next hours passed in a blur. The letter was from the Gravedigger. He wanted money and Brennan was his ransom. In the meantime, she was being kept somewhere. At least, she was as of the date of the letter, the same date of the kidnapping.

As best as the squints could tell, she had been in the car for some time, but she wasn't buried in the car with Hodgins. It was hard for them to determine, because it was her car to begin with. They were sure, however, that Hodgins had sustained injuries, which Zack decided were from the attack that led to his kidnapping, and bled to death while buried. Zack surmised that he probably had several hours of air left, but even if we had found him by the Gravedigger's deadline, he would already have been dead.

Booth stormed FBI headquarters, demanding his badge and gun and command of the taskforce now in search of Doctor Brennan. These were his first sober days in months, but he was sharp and on his game, working non-stop until he got a lead on her location. He was prepared, fully-prepared to do whatever it took to pay the gravedigger's ransom demands, but he didn't want to pay him until he had a solid lead on Bones' location.

A swat team closed in on a location after days of searching and Booth led them inside. They captured the bastard responsible for all of these kidnappings and death. Then they spread out in search of Brennan.

And he found her first. Of course he did. After kicking in dozens of doors, he found the soundproof, airtight room she had been stored in. She hadn't heard anyone coming, so she jumped up from the cot she was laying on in an immediate defensive position.

She looked tired and tattered, but God, she was alive. He threw down the weapon he had been holding and wrapped her in his arms and she melted into him with relief.

"I knew you'd find me. I knew you wouldn't give up," she whispered and Booth just hugged her tighter.

oooooooooooooooooooooooooooooooooooooooooooooooooo

He closed his eyes to absorb the warmth from the sun radiating high above the park on this day. He must have closed them for longer than he thought and dozed off, because he didn't hear their approaching footsteps right away.

He kept his eyes closed as a small hand clamped over his mouth and pinched his nose tight. It was his daughter's new favorite way to wake him up. And he made his silly noises as he gasped for air and attacked her hand with his mouth, making her giggle furiously.

"He's alive, Mommy, he's alive!" the brown-eyed girl gasped through her laughter.

"Thanks for checking on him, baby. I was worried," Brennan said innocently, sitting down next to both of them.

"Are you kidding? Of course I'm alive… I've got these beautiful women in my life to live for," he said, giving his daughter a small toss into the air, enjoying the sounds she made when she was happy.

"Can I go down the slide, Daddy?" she asked, pointing toward the playground.

"Oh, I dunno. What do you think, Mommy?" Booth asked.

"I think it'll cost her," Brennan replied.

"But I don't make any money!" the little girl exclaimed.

"How about I charge you one kiss for me…" Booth said, and his little girl complied. "And a kiss for Mommy…" and that kiss followed as well.

"And another kiss for me," Booth requested, and she promptly squeezed his nose again. "Daaaaaaddy!" she cried. "I can't stay here and give you kisses all day or I'll _never_ ride the slide," she said impatiently.

"Just one more," Booth said, pulling out his best pout. His daughter mimicked a classic Brennan eyeroll but kissed him sweetly once more, before she wiggled out of his arms and ran for the slide.

They sat back and watched her run. Booth raised his arm and put it around Brennan's shoulder, pulling her close.

"You know what today is?" he whispered, and she nodded.

"I know."

"If we hadn't found you… God, Bones, I can't even imagine what my life would be like if you weren't here right now."

"You'd go on, Booth."

"Don't say that Bones."

"No Booth, you would. This life right here, that little girl…" she said, pointing at the playground. "This is your dream, Booth. But if we weren't here, you'd move on. You'd be okay. You'd have to be."

"Bones, stop…"

"You have Parker. You have friends and family who need you, and a balance sheet to work on. Who you are and what you do… even if you hadn't found me in time, I believe you're strong enough to be the man you need to be. Without me. Or maybe for me. You'd survive, Booth."

"Stop saying things like that Bones… life without you… I can't imagine it, Bones. I need you. Now, and always."

"You'll always have me. And you'd survive Booth… you'll survive. Do it for me Booth…"

ooooooooooooooooooooooooooooooooooooooooooo

He didn't know how much time had passed before he was jolted from dream state to consciousness. He thought a noise had woken him, but as he looked around the site, he realized that it was eerily quiet for the number of people who were present.

Beside him, Angela sat. He hadn't seen her when he arrived. And she looked almost as good as he expected he looked. He wanted to feel bad for her. He had the sudden urge to comfort her. But he was far too exhausted to do either. So he just continued to stare straight ahead.

They sat there in silence. And waited.

It may have been minutes or hours before they both heard Zack behind them.

"Angela, Agent Booth?" he said with more caution that one would expect from Zack.

"Is it them, Zack?" Angela asked hoarsely.

Both Angela and Booth turned to face Zack as he answered.

"I've examined the remains in the car…" he said, fidgeting with his hands.

"And?" Booth asked.

"And I can say with a reasonable amount of certainty that the sets of remains are in fact Doctor Hodgins and Doctor Brennan," Zack said.

Behind them, they could hear Cam shouting for Zack from a distance. But their attention remained focused on Zack.

"Are you sure?" Angela whispered morosely.

"While my cursory examination is not conclusive, as I would need to return to the lab, I am confident that the remains in the car belong to them."

"Booth! Angela!" Cam had finally reached them at a full-on sprint from the excavation site.

"Guys… I'm so… I'm so sorry," Cam said breathlessly. "These were in the car, one addressed to each of you," she said, holding up to folded pieces of paper, one with each of their names on it.

Booth's hands were shaking as he grabbed the letter and twirled it around. "I can't… this could be evidence."

"The techs who found the letters looked them over. They didn't see who took them or know anything valuable. The letters are personal, not evidence."

Angela looked at her letter as if she feared the contents. Booth just looked angry. All he had left of her was a crumpled letter?

"I can't… I can't do this… I can't read this here, now. I need… I have to go…" Booth stuttered, walking away from the group.

oooooooooooooooooooooooooooooooooooo

He sat on his barstool and finished his latest glass of scotch. Empty, he slammed it back to the bar and turned to stare at her stool. On the bar in front of her stool sat a letter. A note? A confession? Instructions about where to find her will? Whatever it was, it was something addressed to him.

Her final words.

Another refill appeared in the glass and he grabbed the bartender's arm. Wordlessly, he starred at the bottle until Sparky left it with him.

He finished another glass, having lost count of where he was at. Another and another… and after awhile, she finally appeared.

She smiled at him sadly, tilting her head as if she was waiting for him to speak.

He scoffed at her pointed look and shook his head. "That's all there is. That's all I have left of you," he said, gesturing toward the paper on the bar.

"That's not entirely true," she said. "They found my bones in that car."

"No, they found _my Bones_ in that car."

"That's impossible, you're sitting right here, alive. I'm the one that's… oh. You meant me, _Bones,_ not_ my_ bones,_"_ she said, getting the joke. "That's humorous," she added, grinning.

He just looked at her with this broken sadness that threatened to make her frown. So she tried again.

"You know, you could ask Zack to give you one of my actual bones."

His face went from sad to horrified, "Bones, what the…"

"Archeologists and anthropologists, like my former self, dig up bones all the time to study. We keep them in museums and as relics. You could too. And you could have your pick of bones. Maybe… how about my femur? Right or left, take your pick."

"This is the most absurd conversation I've ever had," Booth said, burying his hands in his face.

"To be fair, this is all happening in your mind. I have no control over what you're thinking," she said, Booth still not looking at her.

"I wouldn't suggest my skull. Given the motif of you apartment, I think people who saw it would have questions you're probably not comfortable answering."

"Bones…"

"Perhaps something small, like one of my phalanx bones. Or something slightly bigger, like a rib. What'll it be Booth, anterior or posterior?"

"None!" he shouted, drawing attention from around the bar to his conversation with himself. "None," he said softer. "I don't want _your_ Bones. I want _my Bones,"_ he emphasized with a defeated sigh.

She sat back sadly and watched him watch her. "I'm always going to be your Bones, Booth. To the rest of the world I was Doctor Temperance Brennan, renowned scientist or best-selling authors. To some, I was Tempe or Bren, a friend or colleague. Others, Temperance, normally to an authority figure at work or school or wherever I called home that month. Hell, I was even a little girl name Joy for some of my life. But I bet you'll never find someone else to be your Bones. Unless, of course you decide to go back to the FBI and work with another forensic anthropologist, I suppose…"

"Not happening."

"Okay. So it's settled. I'm your only Bones."

He threw back another glass of scotch and turned to look at her again.

"You have to read my letter, Booth."

"No."

"Do you remember when you brought me here, during that first case you asked me to help you solve?"

"Nope. I've come here practically every night since you were kidnapped for the ambience."

"That's sarcasm, right?" Brennan said.

"Of course I remember. I also remember you leaving me here and getting in a cab."

"If you'd gotten in the cab with me, we wouldn't be here right now. Or, more accurately, you wouldn't be here right now, talking to yourself."

"What makes you say that?"

"We would have made for a great one-night stand."

"I don't believe that would have been it," Booth said, shaking his head.

"We were drunk. We were drunk and found each other stimulating and we would have satisfied one another and that would have been that. I wasn't ready for more then, and you know you certainly weren't either. No… me, walking away… that was better."

"You didn't speak to me for more than a year after that case."

"But look what happened when I did? For a couple of years, with you, I got out of the lab and started to live. I found out what happened to my mother, I reconnected with my brother. I learned that my Dad is alive. I've helped bring justice to victims whose lives ended too soon."

"Like you," Booth sighed into a sob.

"Like me. There are many, many more people just like me Booth. People who've been murdered and who need you to help bring their killers to justice. You still have more work to do Booth. You can't stop now…"

"But I don't have you. I need my partner. God, I miss my partner."

They were both quiet as he worked up to his last thought.

"I need you, Bones. I just need you. I was… I was just barely getting along before you. And now, I don't know how to do anything without you. I just… I can't."

"I'm here. Not corporeal of course, but I'm here. In your head. When you need me. But… you need to do something for me if you want me to stick around.

"I think you're a ghost. You don't believe in ghosts, yet, here you are."

"There are no such things as ghosts, Booth. Don't be ridiculous."

"If you're only inside my head, I should be able to imagine you whenever I want. But I can't."

"You can. You just need to pick something else. A different trigger. Not that bottle of scotch. Pick another time, another reason other than drunken hallucinations, and I'll be there."

"I don't know what that means?" he said, causing her to laugh.

"I mean, pick something else to trigger your memories. Something ridiculously sentimental, because you like over-romanticized things. Like, when the sun shines or the moon rises, you can think of me. Or when you see your shadow… Maybe when the wind blows…

"Shadows," he drawled out drunkenly. "My shadow is always with me. Sunny or cloud, day or night, inside or outside…"

"Okay. So from now on, when you can see a shadow, you'll be able to see me too. For as long as you need to."

"I'm always going to need to," Booth whispered.

They remained quiet for another moment, until Brennan laughed.

"What's so funny?" Booth asked.

"I'm just wondering, if you see me in your shadow, will there be six more weeks of winter?" she asked, laughing sincerely. "And what about the summer? Surely shadows in the summer don't also correlate somehow to the length of summertime, do they?"

Booth couldn't help but smile. "You are crazy, Doctor Temperance Brennan. My crazy Bones."

"You'll be fine Booth. You'll survive. If not for yourself, then do it for your son. And do it for me."

He leaned in toward her, so close that he could practically feel her forehead on his.

"I can't say goodbye."

"Maybe it's just 'see you later.' You believe in heaven, so maybe I'll be there waiting for you someday."

"You don't believe in heaven…"

"But you do."

"It's not enough…"

"Read my letter, Booth."

"It's the last thing you ever wrote, Bones. This is it."

"Read my letter, Booth."

"Bones…"

"I know I protested it vehemently at first, but the truth is… I really loved being _your_ _Bones_. Almost as much as I loved being your partner. I just really… you know?"

"Bones…" he uttered on a sob.

"Thank you, Booth. For everything."

Booth slammed his fists on to the part and laid his head on top of them as his tears fell freely. "Bones, don't go. Please don't go…"

"I'll see you in the shadows, Booth," she whispered softly.

He lifted his head to look at her, plead with her not to go. But she was already gone.

He choked back a sob as he wiped the tears from his face and went back to starring at his half-filled scotch glass and her letter.

He had a choice.

_He tipped the glass left. Drop. Right. Drop._

He picked the glass up and brought the rim to his lips. But he didn't drink. And he dropped the still half-filled glass to the bar one last time.

He grabbed her letter and walked out of the bar, ignoring the taxis vying for his attention. Tonight, he sought the shadows made by streetlamps to walk home under as he read her final words, knowing that she promised he could find her in them, whenever he needed her.

* * *

_**"I will find a time and place to tell you that you make my life  
messy and confusing and unfocused and irrational and wonderful."**_

* * *

**Thoughts? :)**

**P.S. Merry Christmas to all my ducks. **


End file.
